Starting phenix.real_space_refine on Fri Jun 6 00:24:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hia_34813/06_2025/8hia_34813.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hia_34813/06_2025/8hia_34813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hia_34813/06_2025/8hia_34813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hia_34813/06_2025/8hia_34813.map" model { file = "/net/cci-nas-00/data/ceres_data/8hia_34813/06_2025/8hia_34813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hia_34813/06_2025/8hia_34813.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 20 5.16 5 C 2220 2.51 5 N 620 2.21 5 O 680 1.98 5 H 3660 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 7200 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 360 Classifications: {'peptide': 23} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.60, per 1000 atoms: 0.78 Number of scatterers: 7200 At special positions: 0 Unit cell: (68.85, 114.75, 56.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 O 680 8.00 N 620 7.00 C 2220 6.00 H 3660 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 697.1 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 920 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3660 1.03 - 1.23: 0 1.23 - 1.42: 1300 1.42 - 1.61: 2240 1.61 - 1.80: 40 Bond restraints: 7240 Sorted by residual: bond pdb=" N PRO N 2 " pdb=" CA PRO N 2 " ideal model delta sigma weight residual 1.469 1.479 -0.010 1.28e-02 6.10e+03 6.40e-01 bond pdb=" C GLU F 5 " pdb=" N PRO F 6 " ideal model delta sigma weight residual 1.326 1.337 -0.011 1.44e-02 4.82e+03 5.84e-01 bond pdb=" CA ARG F 13 " pdb=" C ARG F 13 " ideal model delta sigma weight residual 1.529 1.523 0.006 1.04e-02 9.25e+03 3.75e-01 bond pdb=" CA PRO N 2 " pdb=" C PRO N 2 " ideal model delta sigma weight residual 1.520 1.528 -0.008 1.42e-02 4.96e+03 3.32e-01 bond pdb=" CA VAL I 21 " pdb=" CB VAL I 21 " ideal model delta sigma weight residual 1.540 1.548 -0.008 1.36e-02 5.41e+03 3.23e-01 ... (remaining 7235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.70: 11911 0.70 - 1.40: 1178 1.40 - 2.09: 105 2.09 - 2.79: 30 2.79 - 3.49: 16 Bond angle restraints: 13240 Sorted by residual: angle pdb=" N ALA C 4 " pdb=" CA ALA C 4 " pdb=" C ALA C 4 " ideal model delta sigma weight residual 107.73 110.42 -2.69 1.34e+00 5.57e-01 4.03e+00 angle pdb=" N ALA G 4 " pdb=" CA ALA G 4 " pdb=" C ALA G 4 " ideal model delta sigma weight residual 110.80 107.48 3.32 2.13e+00 2.20e-01 2.43e+00 angle pdb=" N ALA D 10 " pdb=" CA ALA D 10 " pdb=" C ALA D 10 " ideal model delta sigma weight residual 108.46 110.73 -2.27 1.51e+00 4.39e-01 2.25e+00 angle pdb=" CA PRO N 2 " pdb=" C PRO N 2 " pdb=" O PRO N 2 " ideal model delta sigma weight residual 120.60 123.10 -2.50 1.82e+00 3.02e-01 1.89e+00 angle pdb=" CA PRO F 6 " pdb=" C PRO F 6 " pdb=" N ASP F 7 " ideal model delta sigma weight residual 115.12 116.81 -1.69 1.25e+00 6.40e-01 1.83e+00 ... (remaining 13235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 3103 16.94 - 33.88: 185 33.88 - 50.82: 64 50.82 - 67.75: 20 67.75 - 84.69: 8 Dihedral angle restraints: 3380 sinusoidal: 1960 harmonic: 1420 Sorted by residual: dihedral pdb=" CB ARG S 13 " pdb=" CG ARG S 13 " pdb=" CD ARG S 13 " pdb=" NE ARG S 13 " ideal model delta sinusoidal sigma weight residual 180.00 120.04 59.96 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA GLU J 1 " pdb=" CB GLU J 1 " pdb=" CG GLU J 1 " pdb=" CD GLU J 1 " ideal model delta sinusoidal sigma weight residual -180.00 -120.46 -59.54 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA GLU Q 1 " pdb=" CB GLU Q 1 " pdb=" CG GLU Q 1 " pdb=" CD GLU Q 1 " ideal model delta sinusoidal sigma weight residual 180.00 -121.04 -58.96 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 3377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 343 0.024 - 0.048: 130 0.048 - 0.072: 48 0.072 - 0.096: 14 0.096 - 0.120: 125 Chirality restraints: 660 Sorted by residual: chirality pdb=" CA VAL S 17 " pdb=" N VAL S 17 " pdb=" C VAL S 17 " pdb=" CB VAL S 17 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA VAL D 17 " pdb=" N VAL D 17 " pdb=" C VAL D 17 " pdb=" CB VAL D 17 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.52e-01 chirality pdb=" CA VAL I 14 " pdb=" N VAL I 14 " pdb=" C VAL I 14 " pdb=" CB VAL I 14 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.46e-01 ... (remaining 657 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 5 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO D 6 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 6 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 6 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU L 5 " 0.007 5.00e-02 4.00e+02 1.08e-02 1.87e-01 pdb=" N PRO L 6 " -0.019 5.00e-02 4.00e+02 pdb=" CA PRO L 6 " 0.005 5.00e-02 4.00e+02 pdb=" CD PRO L 6 " 0.006 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 5 " 0.001 2.00e-02 2.50e+03 2.85e-03 8.11e-02 pdb=" C GLU D 5 " -0.005 2.00e-02 2.50e+03 pdb=" O GLU D 5 " 0.002 2.00e-02 2.50e+03 pdb=" N PRO D 6 " 0.002 2.00e-02 2.50e+03 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 942 2.27 - 2.86: 15845 2.86 - 3.44: 15591 3.44 - 4.02: 20552 4.02 - 4.60: 29975 Nonbonded interactions: 82905 Sorted by model distance: nonbonded pdb=" OD1 ASP S 7 " pdb=" H MET S 9 " model vdw 1.694 2.450 nonbonded pdb=" HG1 THR G 19 " pdb=" OE1 GLN L 23 " model vdw 1.793 2.450 nonbonded pdb=" O ASN L 12 " pdb="HD22 ASN P 12 " model vdw 1.802 2.450 nonbonded pdb=" O ARG B 13 " pdb="HH11 ARG R 13 " model vdw 1.819 2.450 nonbonded pdb=" H1 GLU R 1 " pdb=" OE2 GLU S 1 " model vdw 1.834 2.450 ... (remaining 82900 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.870 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0837 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.012 3580 Z= 0.067 Angle : 0.359 3.489 4920 Z= 0.166 Chirality : 0.054 0.120 660 Planarity : 0.001 0.029 640 Dihedral : 15.833 84.693 1340 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.14 % Favored : 87.62 % Rotamer: Outliers : 2.86 % Allowed : 13.57 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.29), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.22), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS R 16 ARG 0.001 0.000 ARG P 13 Details of bonding type rmsd covalent geometry : bond 0.00129 ( 3580) covalent geometry : angle 0.35911 ( 4920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 5 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.030 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. REVERT: A 20 ASN cc_start: 0.5496 (m-40) cc_final: 0.4892 (p0) outliers start: 1 outliers final: 1 residues processed: 4 average time/residue: 0.1188 time to fit residues: 0.5376 Evaluate side-chains 4 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 31 optimal weight: 0.0570 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.151293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.121730 restraints weight = 2226.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.127563 restraints weight = 1035.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.131574 restraints weight = 601.262| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3443 moved from start: 3.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.055 3580 Z= 0.508 Angle : 1.455 8.433 4920 Z= 0.837 Chirality : 0.076 0.242 660 Planarity : 0.006 0.019 640 Dihedral : 9.520 20.864 480 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 39.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.76 % Allowed : 23.81 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.006 HIS H 16 ARG 0.002 0.001 ARG K 13 Details of bonding type rmsd covalent geometry : bond 0.01220 ( 3580) covalent geometry : angle 1.45476 ( 4920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 5 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.027 Fit side-chains TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 5 average time/residue: 0.0694 time to fit residues: 0.4134 Evaluate side-chains 2 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.156204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.120122 restraints weight = 1143.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.122377 restraints weight = 453.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.123557 restraints weight = 282.981| |-----------------------------------------------------------------------------| r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3376 moved from start: 3.6420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.043 3580 Z= 0.368 Angle : 0.920 4.734 4920 Z= 0.533 Chirality : 0.051 0.110 660 Planarity : 0.013 0.055 640 Dihedral : 7.165 17.382 480 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 36.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.76 % Allowed : 4.76 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.47 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.008 HIS E 16 ARG 0.001 0.001 ARG L 13 Details of bonding type rmsd covalent geometry : bond 0.00805 ( 3580) covalent geometry : angle 0.92026 ( 4920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 5 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.028 Fit side-chains TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. REVERT: T 9 MET cc_start: 0.3850 (mmt) cc_final: 0.3276 (mmm) outliers start: 1 outliers final: 1 residues processed: 5 average time/residue: 0.0827 time to fit residues: 0.4833 Evaluate side-chains 4 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.153476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.111906 restraints weight = 1319.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.114367 restraints weight = 650.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.115341 restraints weight = 469.171| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3358 moved from start: 3.7205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3580 Z= 0.259 Angle : 0.794 4.129 4920 Z= 0.458 Chirality : 0.051 0.118 660 Planarity : 0.008 0.036 640 Dihedral : 6.858 20.162 480 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 28.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.76 % Allowed : 4.76 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.03 (0.29), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.22), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.005 HIS D 16 ARG 0.001 0.000 ARG T 13 Details of bonding type rmsd covalent geometry : bond 0.00571 ( 3580) covalent geometry : angle 0.79410 ( 4920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 4 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.028 Fit side-chains TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. REVERT: T 9 MET cc_start: 0.4148 (mmt) cc_final: 0.3602 (mmm) outliers start: 1 outliers final: 1 residues processed: 4 average time/residue: 0.0842 time to fit residues: 0.3948 Evaluate side-chains 4 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 13 optimal weight: 0.0070 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.130628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.107034 restraints weight = 1534.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.109918 restraints weight = 743.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.111677 restraints weight = 445.326| |-----------------------------------------------------------------------------| r_work (final): 0.4342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2970 moved from start: 3.7630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 3580 Z= 0.188 Angle : 0.688 3.762 4920 Z= 0.391 Chirality : 0.050 0.120 660 Planarity : 0.008 0.030 640 Dihedral : 5.407 14.167 480 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.76 % Allowed : 4.76 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.17 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.002 HIS P 16 ARG 0.000 0.000 ARG B 13 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 3580) covalent geometry : angle 0.68760 ( 4920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 714 Ramachandran restraints generated. 357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 7 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 6 time to evaluate : 0.029 Fit side-chains TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 7 average time/residue: 0.3389 time to fit residues: 2.4405 Evaluate side-chains 4 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 17 optimal weight: 0.0370 chunk 30 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 16 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.110690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.093506 restraints weight = 1620.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.097589 restraints weight = 743.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.100538 restraints weight = 423.426| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2872 moved from start: 3.8034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 3580 Z= 0.323 Angle : 1.045 4.923 4920 Z= 0.576 Chirality : 0.050 0.102 660 Planarity : 0.021 0.113 640 Dihedral : 6.747 19.537 480 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 37.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.76 % Allowed : 0.00 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.96 (0.28), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.21), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.012 HIS P 16 ARG 0.007 0.004 ARG L 13 Details of bonding type rmsd covalent geometry : bond 0.00810 ( 3580) covalent geometry : angle 1.04478 ( 4920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 5 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.033 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. REVERT: H 9 MET cc_start: 0.5016 (tpt) cc_final: 0.4586 (mmm) outliers start: 1 outliers final: 1 residues processed: 4 average time/residue: 0.5073 time to fit residues: 2.0914 Evaluate side-chains 4 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.107174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.091582 restraints weight = 1771.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.094553 restraints weight = 993.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.096558 restraints weight = 607.214| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3365 moved from start: 3.8496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.060 3580 Z= 0.357 Angle : 0.891 4.210 4920 Z= 0.510 Chirality : 0.053 0.114 660 Planarity : 0.015 0.082 640 Dihedral : 7.862 18.163 480 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 49.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.76 % Allowed : 0.00 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.69 (0.29), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.33 (0.22), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.008 HIS A 16 ARG 0.003 0.001 ARG O 13 Details of bonding type rmsd covalent geometry : bond 0.00851 ( 3580) covalent geometry : angle 0.89144 ( 4920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 5 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.033 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 4 average time/residue: 0.4894 time to fit residues: 2.0224 Evaluate side-chains 4 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.119922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.097549 restraints weight = 1840.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.100056 restraints weight = 1169.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.101856 restraints weight = 847.396| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3761 moved from start: 3.9203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.067 3580 Z= 0.343 Angle : 1.010 5.138 4920 Z= 0.545 Chirality : 0.052 0.114 660 Planarity : 0.015 0.075 640 Dihedral : 7.953 19.776 480 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 47.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.76 % Allowed : 4.76 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.16 (0.28), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.69 (0.22), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.003 HIS L 16 ARG 0.000 0.000 ARG J 13 Details of bonding type rmsd covalent geometry : bond 0.00883 ( 3580) covalent geometry : angle 1.00957 ( 4920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 4 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 3 time to evaluate : 0.029 Fit side-chains TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. REVERT: L 7 ASP cc_start: 0.8042 (p0) cc_final: 0.7748 (p0) outliers start: 1 outliers final: 1 residues processed: 4 average time/residue: 0.4463 time to fit residues: 1.8487 Evaluate side-chains 3 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.136359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.112423 restraints weight = 2034.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.114802 restraints weight = 1062.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.116529 restraints weight = 686.163| |-----------------------------------------------------------------------------| r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3475 moved from start: 3.9815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 3580 Z= 0.337 Angle : 0.920 5.825 4920 Z= 0.512 Chirality : 0.054 0.143 660 Planarity : 0.009 0.042 640 Dihedral : 9.760 22.130 480 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 39.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 4.76 % Allowed : 0.00 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.40 (0.28), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.87 (0.22), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.003 HIS M 16 ARG 0.007 0.003 ARG Q 13 Details of bonding type rmsd covalent geometry : bond 0.00833 ( 3580) covalent geometry : angle 0.91986 ( 4920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 5 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.028 Fit side-chains TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 5 average time/residue: 0.3912 time to fit residues: 2.0193 Evaluate side-chains 3 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 2 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.168755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.125502 restraints weight = 4516.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.130590 restraints weight = 2901.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.134336 restraints weight = 2135.460| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3649 moved from start: 3.9155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 3580 Z= 0.348 Angle : 1.299 10.334 4920 Z= 0.675 Chirality : 0.059 0.204 660 Planarity : 0.041 0.223 640 Dihedral : 11.338 34.658 480 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 66.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.05 % Favored : 80.95 % Rotamer: Outliers : 4.76 % Allowed : 0.00 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.80 (0.26), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.18 (0.20), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.004 HIS I 16 ARG 0.038 0.019 ARG F 13 Details of bonding type rmsd covalent geometry : bond 0.00845 ( 3580) covalent geometry : angle 1.29921 ( 4920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** TARDY: cannot create tardy model for: "GLN A 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN C 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN D 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN E 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN G 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN I 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN K 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN M 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN N 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN O 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN P 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Q 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN R 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN S 23 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. Evaluate side-chains 5 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.033 Fit side-chains TARDY: cannot create tardy model for: "GLN T 23 " (corrupted residue). Skipping it. REVERT: T 9 MET cc_start: 0.4650 (mmm) cc_final: 0.3716 (mmt) outliers start: 1 outliers final: 1 residues processed: 5 average time/residue: 0.0974 time to fit residues: 0.5555 Evaluate side-chains 2 residues out of total 21 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.137935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.105049 restraints weight = 1497.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.108433 restraints weight = 716.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.110366 restraints weight = 461.939| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3273 moved from start: 3.9698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 3580 Z= 0.289 Angle : 1.223 9.429 4920 Z= 0.629 Chirality : 0.055 0.146 660 Planarity : 0.035 0.191 640 Dihedral : 10.608 30.140 480 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 60.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.76 % Allowed : 4.76 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.97 (0.24), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.31 (0.18), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS P 16 ARG 0.036 0.018 ARG J 13 Details of bonding type rmsd covalent geometry : bond 0.00715 ( 3580) covalent geometry : angle 1.22331 ( 4920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1876.24 seconds wall clock time: 32 minutes 43.52 seconds (1963.52 seconds total)